Bioconductor LfcThreshold

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1.9k

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DESeq2 lfcThreshold

2.3 years ago Abir.khazaal ▴ 10

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lfcshrink DESeq2 RNASeq lfcthreshold

2.5 years ago ClaudiaE • 0

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2.5k

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ashr Deseq2 lfcThreshold

updated 3.3 years ago by Michael Love 43k • written 4.7 years ago by Iryna • 0

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8.5k

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deseq2 differential expression logfoldchange lfcshrink lfcthreshold

updated 3.6 years ago by Michael Love 43k • written 6.5 years ago by emi.sch ▴ 40

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1.2k

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deseq2 lfcshrink lfcthreshold differential gene expression

updated 6.1 years ago by Michael Love 43k • written 6.1 years ago by corentinrichard374369 • 0

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DESeq2 lfcThreshold

updated 6.8 years ago by Michael Love 43k • written 6.8 years ago by Mike ▴ 10

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6.0k

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lfcthreshold deseq2

updated 7.0 years ago by Michael Love 43k • written 7.0 years ago by lirongrossmann ▴ 80

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3.3k

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deseq2 microrna lfcThreshold stable expression ffpe

updated 9.2 years ago by Michael Love 43k • written 9.2 years ago by mariakarand ▴ 20

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Comment: minfi latest update for EPIC V2 chip by macdonaldfrench7286566 • 0

Yes, the most updated analysis for the EPIC V2 chip using the minfi package still involves using the annotations provided by jokergoo. *Th…

Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

To compute CPM values from edgeR: ``` y <- DGEList(counts = counts, samples = samples, genes = genes, group = samples$Disease_status) y <- …

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k

Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0

But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…

Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0

After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```

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A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor

A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio

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